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Online Journal of Bioinformatics © 


Volume 9 (1): 78-91, 2008.

Identification of SSR-ESTs corresponding to alkaloid, phenylpropanoid and terpenoid biosynthesis in MAPís.


 Tripathi KP, Roy S, Khan F, Shasany AK, Sharma A, Khanuja SPS


Bioinformatics & In Silico Biology Division, Central Institute of Medicinal & Aromatic Plants (CSIR), P.O. CIMAP, Lucknow-226015 (UP), India.




Tripathi KP, Roy S, Khan F, Shasany AK, Sharma A, Khanuja SPS., Identification of SSR-ESTs corresponding to alkaloid, phenylpropanoid and terpenoid biosynthesis in MAPís, On J Bioinform., 9 (1): 78-91, 2008. Simple sequence repeats (SSRs) are repetitions of nucleotide motifs of 1 to 5 bases and are currently the markers of choice in many plants and animals genomes. SSRs are the DNA regions where a few bases are tandemly repeated. SSRs have been proven to be the markers of choice in plants genetics research and for breeding purposes because of their hyper-variability and ease of detection. However, development of these markers is expensive, labour intensive and time consuming, if they are being developed from genomic libraries. In this study, SSRs were mined in silico from ESTs of medicinal and aromatic plants (MAPs) corresponding to secondary metabolites e.g. Alkaloids, Phenylpropanoids and Terpenoids. SSRs are potential candidates for markers, gene tagging, comparative genomics research and breeding purposes. For this, comparative genomic study was performed for finding the corresponding genes to these SSR-ESTs using Arabidopsis thaliana as a model organism.  Results revealed that the SSRs e.g., 941 trinucleotides, 213 dinucleotides, 157 tetranucleotides and 179 pentanucleotides were distributed throughout the studied datasets of ESTs in medicinal plants viz., Coptis japonica, Oryza sativa, Papaver somniferum, Catharanthus roseus, Phaseolus vulgaris, Capsicum annuum, Mentha piperita and Euphorbia tirucalli. Primers associated with the SSR-ESTs were also designed successfully. Moreover, functional perspectives of these SSRs suggest that microsatellites are more than mere repetitive sequences and their role have been attributed to many biological functions. Because of their abundance and high polymorphism, microsatellites could be widely used to develop genetic markers for the construction of linkage maps of medicinal crops.


Keywords: ESTs, SSRs, Microsatellites, Primers, Markers, Secondary metabolites, Alkaloids, Phenylpropanoids, Terpenoids, Medicinal & Aromatic Plants.